Magnetic chitin beads (MCB) coated with reveals transcriptome dynamics in adult mice with a complex gut microbiota.

adapts to the host environment by altering gene expression. Because of the complexity of the gut microbiome, current transcriptome studies have focused on microbiota-undeveloped conditions, neglecting the interaction between the host's commensal gut microbiota and . In this study, we analyzed the transcriptome of fully colonized adult mice using coated-magnetic chitin beads (vcMCB). This provides a simple yet powerful method for obtaining high-quality RNA from during colonization in mice. The transcriptome of recovered from adult mice infected with vcMCB shows differential expression of several genes when compared to recovered from the infant mouse and infant rabbit model. Some of these genes were also observed to be differentially expressed in previous studies of recovered from human infection when compared to grown . In particular, we confirmed that resists the inhibitory effects of low pH and formic acid from gut microbiota, such as and , by downregulating . We propose that the product may protect from formic acid stress through a novel acid tolerance response mechanism. Transcriptomic data obtained using the vcMCB system provide new perspectives on the interaction between and the gut microbiota, and this approach can also be applied to studies of other pathogenic bacteria.